The Preparation of Allosteric SYK Inhibitor X1 and Investigation of a Covalent Inhibition Mechanism

Posted onAuthorFrances PotjewydLeave a comment

Frances M. Potjewyd and Vittorio Katis http://doi.org/10.5281/zenodo.4670214 Spleen Tyrosine Kinase (SYK) has a reported role in AD pathology and was identified as a target for the TREAT-AD (Target Enablement to Accelerate Therapy Development for Alzheimer’s Disease) program.1–3 We are focusing drug discovery efforts on the inhibition of SYK and more specifically, inhibition of the interaction Read More …

Preparation of the Soluble Epoxide Inhibitor SWE101 and the DOCK1 inhibitor TBOPP

Posted onAuthorDavid RogersLeave a comment

Preparation of the Soluble Epoxide Inhibitor SWE101 and the DOCK1 inhibitor TBOPP David A. Rogers and Kevin J. Frankowski https://doi.org/10.5281/zenodo.4637834 The National Institute on Aging has made a significant commitment to improving the treatment of Alzheimer’s disease through the funding of the TREAT-AD network (Target Enablement to Accelerate Therapy Development for AD, https://treatad.org/). One of Read More …

Druggability and Amino Acid Variability of the Catalytic Site of SARS-CoV-2 Nsp15 Across Coronaviruses and SARS-CoV-2 Samples – Post 26

Posted onAuthorSetayesh Yazdani3 Comments

Today’s post focuses on another protein encoded by many coronaviruses, the non-structural protein 15 (nsp15), an endoribonuclease. Nsp15 is a nidoviral RNA uridylate-specific endoribonuclease (NendoU) with C-terminal catalytic activity. This protein belongs to the EndoU family, and they all carry an RNA endonuclease activity to produce 2’-3’ cyclic phosphodiester and 5’-hydroxyl termini. (Kim et al. Read More …

Druggability and Genetic Variability at nsp9 Peptide-bound Pockets and Beta-barrel Pockets Across Coronaviruses and SARS-CoV-2 Samples – Post 25

Posted onAuthorSetayesh YazdaniLeave a comment

Today’s post focuses on another protein encoded in open reading frame 1a (ORF1a) of many coronaviruses, the non-structural protein 9 (nsp9). Nsp9 is thought to mediate viral replication. In SARS-CoV-1, nsp9’s role has been highlighted as a single-stranded RNA-binding subunit. (Egloff et al., 2004) The structure of SARS-CoV-2 nsp9 was solved in both apo and Read More …

Druggability and Genetic Variability of the Catalytic and Allosteric Sites of SARS-CoV-2 nsp14 Across Coronaviruses and SARS-CoV-2 Samples – Post 24

Posted onAuthorSetayesh YazdaniLeave a comment

Hello and happy new year! I am back from my winter break and starting to get back to research. If you have followed my previous posts, you know that I have posted the druggability and genetic variability analysis of several protein targets of SARS-CoV-2. There are a few targets that I will be posting in Read More …

Project Overview: Introduction to WDR12 and WDR55 Proteins

Posted onAuthorFang-Chi ChangLeave a comment

I am currently completing my fourth-year thesis in Dr. Dalia Barsyte-Lovejoy’s lab. I have a strong interest in both pharmacology and biochemistry. I am interested in learning about biochemical pathways in the body, with the goal of finding compounds that can target those pathways and for them to potentially develop into therapeutics. My project focuses Read More …

Distinguishing between catalytic and non-catalytic pockets in the ligandable human genome

Posted onAuthorEvianne RoversLeave a comment

My goal is to find druggable pockets in human enzymes that are non-catalytic. These non-catalytic druggable pockets may then be exploited for proximity pharmacology (ProxPharm), a novel paradigm in drug discovery where chimeric compounds bring two proteins in close proximity to elicit an effect of one protein on the other1. For example, PROTACs simultaneously bind Read More …

Druggability and Genetic Variability of the ATPase Site and Central Channel of SARS-CoV-2 nsp13 Helicase Across Coronaviruses and SARS-CoV-2 Samples – Post 23

Posted onAuthorSetayesh Yazdani2 Comments

One of the important enzymes in the replication cycle of the SARS-CoV-2 virus is the helicase, which is also known as non-structural protein 13 (nsp13). During the viral life cycle, the holo-RNA-dependent RNA polymerase, also known as nsp12, is thought to coordinate with several additional factors, including the nsp13 helicase (Snijder et al., 2016; Sola Read More …

Druggability and Genetic Variability of the ADP-bound Pocket of SARS-CoV-2 RNA-dependent RNA polymerase NiRAN domain Across Coronaviruses and SARS-CoV-2 Samples – Post 22

Posted onAuthorSetayesh YazdaniLeave a comment

The RNA-dependent RNA-polymerase (RdRp) also known as non-structural protein 12 (nsp12) is the target of antiviral agent remdesivir. Nsp12 has an important role in viral genome replication and transcription. (Chen et al., 2020)  Chen et al. identified a new pocket on the N-terminal extension of nsp12 occupied by ADP-Mg2+ after solving the structure of the helicase-polymerase complex. This ADP-bound pocket is on the N-terminal nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain which Read More …